I've seen similar boot problems before on systems that had something wrong with the boot.ini file, like a deleted "default=" entry or an inaccurate ARC path.
When the default entry is missing the computer will display "NT (default)" as a boot menu choice, and it will use
multi(0)disk(0)partition(1)\WINNT
as the ARC path. If the NT system is not where the system expects to find it, the computer will fail to boot and give the missing ntoskrnl.exe message.
Is anyone or anything messing with your boot.ini file? I have seen some pretty weird stuff happen with boot.ini files, particularly when there was some arcane parsing problem caused by a non-ASCII character embedded somewhere in the file.
BTW, when using the repair system files option in NT4 you have to remember to reapply the service pack. I have heard rumors, but have seen no real evidence, that this may also be true with W2K. System File Protection in W2K is supposed to eliminate the need to do this, of course.
Hope you solve the mystery, and let us know what was causing the behavior.
Regards,
Jim